pyROX.line_by_line.lbl ====================== .. py:module:: pyROX.line_by_line.lbl Classes ------- .. autoapisummary:: pyROX.line_by_line.lbl.LineProfileHelper pyROX.line_by_line.lbl.LineByLine Module Contents --------------- .. py:class:: LineProfileHelper Helper class for line profile calculations. .. py:method:: compute_line_strength(T, S_0, E_low, nu_0) Calculates the line strength for a given temperature. :param T: Temperature in Kelvin. :type T: float :param S_0: Line strength at reference temperature. :type S_0: float :param E_low: Lower state energy in Joules. :type E_low: float :param nu_0: Transition frequency in s^-1. :type nu_0: float :returns: Line strength in s^-1/(molecule m^-2). :rtype: float .. py:method:: normalise_wing_cutoff(S, cutoff_distance, gamma_L) Normalises the line strength to account for wing cutoff. :param S: Line strengths. :type S: array :param cutoff_distance: Distance for wing cutoff. :type cutoff_distance: float :param gamma_L: Lorentzian widths. :type gamma_L: array :returns: Normalised line strengths. :rtype: array .. py:method:: pressure_shift(P, T, nu_0, delta=None) Applies pressure shift to the transition frequency. :param P: Pressure in Pa. :type P: float :param T: Temperature in Kelvin. :type T: float :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param delta: Pressure shift coefficient. :type delta: float, optional :returns: Pressure-shifted frequencies. :rtype: array .. py:method:: compute_vdw_broadening(P, T, E_low, **kwargs) Calculates Van der Waals broadening. :param P: Pressure in Pa. :type P: float :param T: Temperature in Kelvin. :type T: float :param E_low: Lower state energy in Joules. :type E_low: float :param \*\*kwargs: Additional parameters. :returns: Van der Waals broadening in s^-1. :rtype: float .. py:method:: compute_natural_broadening(A) Calculates natural broadening. :param A: Einstein A-coefficient in s^-1. :type A: float :returns: Natural broadening in s^-1. :rtype: float .. py:method:: compute_doppler_broadening(T, nu_0) Calculates Doppler broadening. :param T: Temperature in Kelvin. :type T: float :param nu_0: Transition frequency in s^-1. :type nu_0: float :returns: Doppler broadening in s^-1. :rtype: float .. py:method:: compute_lorentz_width(gamma_vdW, gamma_N) Calculates Lorentzian width. :param gamma_vdW: Van der Waals broadening in s^-1. :type gamma_vdW: float :param gamma_N: Natural broadening in s^-1. :type gamma_N: float :returns: Lorentzian width in s^-1. :rtype: float .. py:method:: compute_voigt_width(gamma_G, gamma_L) Calculates Voigt width. :param gamma_G: Gaussian width in s^-1. :type gamma_G: float :param gamma_L: Lorentzian width in s^-1. :type gamma_L: float :returns: Voigt width in s^-1. :rtype: float .. py:method:: _bin_transitions_for_local_cutoff(nu_0) Bins the transitions to the nearest sub-sampled grid point. :param nu_0: Transition frequencies in s^-1. :type nu_0: array :returns: Indices of transitions per bin. :rtype: array .. py:method:: apply_local_cutoff(S, nu_0, factor) Applies local cutoff to line strengths. Retain lines with a certain fraction of cumulative strength. :param S: Line strengths. :type S: array :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param factor: Fraction of cumulative strength to retain. :type factor: float :returns: Modified line strengths. :rtype: array .. py:method:: calculate_line_profiles(nu_0, S, gamma_L, gamma_G, nu_grid, wing_cutoff_distance, delta_nu) Calculates line profiles in chunks to optimise speed. :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param S: Line strengths. :type S: array :param gamma_L: Lorentzian widths. :type gamma_L: array :param gamma_G: Gaussian widths. :type gamma_G: array :param nu_grid: Wavenumber grid. :type nu_grid: array :param wing_cutoff_distance: Wing cutoff distance in s^-1. :type wing_cutoff_distance: float :param delta_nu: Wavenumber grid spacing in s^-1. :type delta_nu: float :returns: Opacity cross-section on the grid. :rtype: array .. py:method:: _calculate_line_profiles_one_by_one(nu_0, strength, y, gamma_G, nu_grid, slice_nu_grid) Calculates line profiles one by one. :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param strength: Line strengths. :type strength: array :param y: Complex part of Faddeeva coordinate. :type y: array :param gamma_G: Gaussian widths. :type gamma_G: array :param nu_grid: Wavenumber grid. :type nu_grid: array :param slice_nu_grid: Slices of the wavenumber grid. :type slice_nu_grid: array :returns: Opacity cross-section on the grid. :rtype: array .. py:method:: _calculate_line_profiles_in_chunks(nu_0, S, gamma_L, gamma_G, nu_grid, wing_cutoff_distance, delta_nu, N_lines_in_chunk=1) Calculates line profiles in chunks to optimise speed. :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param S: Line strengths. :type S: array :param gamma_L: Lorentzian widths. :type gamma_L: array :param gamma_G: Gaussian widths. :type gamma_G: array :param nu_grid: Wavenumber grid. :type nu_grid: array :param wing_cutoff_distance: Wing cutoff distance in s^-1. :type wing_cutoff_distance: float :param delta_nu: Wavenumber grid spacing in s^-1. :type delta_nu: float :param N_lines_in_chunk: Number of lines to process in each chunk. :type N_lines_in_chunk: int :returns: Opacity cross-section on the grid. :rtype: array .. py:method:: _calculate_line_profiles_in_chunks_fixed_delta_nu(nu_0, S, gamma_L, gamma_G, nu_grid, wing_cutoff_distance, delta_nu, N_lines_in_chunk=1) Calculates line profiles for a fixed wavenumber spacing. This method is more efficient than calculate_line_profiles_in_chunks(). :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param S: Line strengths. :type S: array :param gamma_L: Lorentzian widths. :type gamma_L: array :param gamma_G: Gaussian widths. :type gamma_G: array :param nu_grid: Wavenumber grid. :type nu_grid: array :param wing_cutoff_distance: Wing cutoff distance in s^-1. :type wing_cutoff_distance: float :param delta_nu: Wavenumber grid spacing in s^-1. :type delta_nu: float :param N_lines_in_chunk: Number of lines to process in each chunk. :type N_lines_in_chunk: int :returns: Opacity cross-section on the grid. :rtype: array .. py:class:: LineByLine(config, **kwargs) Bases: :py:obj:`pyROX.CrossSections`, :py:obj:`LineProfileHelper` Base class for line-by-line cross-sections. .. py:method:: _read_configuration_parameters(config) Reads parameters specific to line-by-line calculations from the configuration. :param config: Configuration object containing parameters. :type config: object .. py:method:: _read_equation_of_state() Reads the equation of state for the gas mixture. .. py:method:: _read_mass() Reads the mass of the species from the configuration or database. .. py:method:: _read_pressure_broadening_info() Reads the pressure broadening parameters from the configuration. .. py:method:: _read_partition_function() Reads the partition function from the configuration file. .. py:method:: iterate_over_PT_grid(function, progress_bar=True, **kwargs) Iterates over the pressure-temperature grid and apply a function. :param function: Function to apply at each grid point. :type function: callable :param progress_bar: Whether to show a progress bar. :type progress_bar: bool :param \*\*kwargs: Additional arguments for the function. .. py:method:: calculate_cross_sections(P, T, nu_0, S_0, E_low, A, delta=None, **kwargs) Computes the cross-sections for given parameters. :param P: Pressure in Pa. :type P: float :param T: Temperature in Kelvin. :type T: float :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param S_0: Line strengths at reference temperature. :type S_0: array :param E_low: Lower state energies in Joules. :type E_low: array :param A: Einstein A-coefficients in s^-1. :type A: array :param delta: Pressure shift coefficients. :type delta: array, optional :param \*\*kwargs: Additional arguments. .. py:method:: calculate_temporary_outputs(overwrite=False, save_in_one_file=False, files_range=None, **kwargs) Calculates temporary outputs for cross-sections. :param overwrite: Whether to overwrite existing files. :type overwrite: bool :param save_in_one_file: Whether to save all outputs in one file. :type save_in_one_file: bool :param files_range: Range of files to process. :type files_range: tuple, optional :param \*\*kwargs: Additional arguments. .. py:method:: save_combined_outputs(**kwargs) Saves the merged outputs to a file. :param \*\*kwargs: Additional arguments for saving. .. py:method:: plot_combined_outputs(fig=None, ax=None, return_fig_ax=False, cmaps=['coolwarm', 'viridis'], xscale='log', yscale='log', xlim=None, ylim=None, ls='-', lw=0.7, **kwargs) Plots the merged outputs. :param fig: Figure object for plotting. :type fig: matplotlib.figure.Figure :param ax: Axes object for plotting. :type ax: matplotlib.axes.Axes :param return_fig_ax: Whether to return the figure and axes. :type return_fig_ax: bool :param cmaps: List of colormaps for plotting. :type cmaps: list :param xscale: Scale for the x-axis. :type xscale: str :param yscale: Scale for the y-axis. :type yscale: str :param xlim: Limits for the x-axis. :type xlim: tuple, optional :param ylim: Limits for the y-axis. :type ylim: tuple, optional :param ls: Line style for plotting. :type ls: str :param \*\*kwargs: Additional arguments for plotting. .. py:method:: convert_to_pRT3(contributor=None, **kwargs) Converts the cross-sections to petitRADTRANS v3.0 format. :param contributor: Name of the contributor for these data. :type contributor: str :param \*\*kwargs: Additional arguments for conversion. :raises ValueError: If required metadata is missing in the configuration. :raises KeyError: If required keys are missing in the metadata.